Hemispheroidal domes (microbialites) produced by natural populations of filamentous cyanobacteria belonging to four distinct Phormidium species, and one probable new species of Schizothrix, were collected alive from 0 to 25 m depth habitats in the lagoon of Tikehau atoll (Tuamotu, French Polynesia). This study establishes the biochemical controls on in situ carbonate precipitation processes ("organomineralization" processes) occurring merely in the alveolate network of non-coalescent microfibrils that characterizes the degraded parts of the microbialite domes. Comparison is made between amino-acid and monosaccharide composition of purified cyanobacterially produced organic matter and that of intramineral (soluble and insoluble) organic matrices associated with carbonate precipitates. The results emphasize the importance of dicarboxylic (aspartic and glutamic) acids, released by the decay of cyanobacterial sheaths, in CaCO3 formation and demonstrates that the in situ precipitation of ultra-fine micrites is a highly selective process regarding the available external organic matter. This diagenetic process is thought to result from incipient hydrolysis of cyanobacterial S-layer proteins attached to extracellular polysaccharide fibrils composing the sheath. Taxonomic affinity of cyanobacterial populations responsible for microbialite construction is one of the major factors allowing biochemical discrimination of in situ precipitated carbonates, indicating that specific mucilages or their degradational products are guiding forces for the calcification processes. Another possible source for the formation of carbonate-associated organic matrices is derived from metabolites (e.g., mucus) released in water by lagoon-dwelling benthic organisms.